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<a href="Bio-module.html">Package Bio</a> ::
Package SeqUtils
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package SeqUtils</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqUtils-pysrc.html">source code</a></span></p>
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<li> <strong class="uidlink"><a href="Bio.SeqUtils.CheckSum-module.html">Bio.SeqUtils.CheckSum</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CodonUsage-module.html">Bio.SeqUtils.CodonUsage</a></strong> </li>
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<a href="Bio.SeqUtils.ProteinX-class.html" class="summary-name">ProteinX</a>
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<td><span class="summary-sig"><a href="Bio.SeqUtils-module.html#reverse" class="summary-sig-name">reverse</a>(<span class="summary-sig-arg">seq</span>)</span><br />
Reverse the sequence.</td>
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<td><span class="summary-sig"><a name="GC"></a><span class="summary-sig-name">GC</span>(<span class="summary-sig-arg">seq</span>)</span><br />
calculates G+C content</td>
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<td><span class="summary-sig"><a name="GC123"></a><span class="summary-sig-name">GC123</span>(<span class="summary-sig-arg">seq</span>)</span><br />
calculates total G+C content plus first, second and third position</td>
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<td><span class="summary-sig"><a name="GC_skew"></a><span class="summary-sig-name">GC_skew</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">window</span>=<span class="summary-sig-default">100</span>)</span><br />
calculates GC skew (G-C)/(G+C)</td>
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<td><span class="summary-sig"><a name="xGC_skew"></a><span class="summary-sig-name">xGC_skew</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">window</span>=<span class="summary-sig-default">1000</span>,
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<span class="summary-sig-arg">px</span>=<span class="summary-sig-default">100</span>,
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calculates and plots normal and accumulated GC skew (GRAPHICS !!!)</td>
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<td><span class="summary-sig"><a name="molecular_weight"></a><span class="summary-sig-name">molecular_weight</span>(<span class="summary-sig-arg">seq</span>)</span></td>
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<td><span class="summary-sig"><a name="nt_search"></a><span class="summary-sig-name">nt_search</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">subseq</span>)</span><br />
search for a DNA subseq in sequence use ambiguous values (like N = A
or T or C or G, R = A or G etc.) searches only on forward strand</td>
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<td><span class="summary-sig"><a name="makeTableX"></a><span class="summary-sig-name">makeTableX</span>(<span class="summary-sig-arg">table</span>)</span></td>
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<td><span class="summary-sig"><a href="Bio.SeqUtils-module.html#seq3" class="summary-sig-name">seq3</a>(<span class="summary-sig-arg">seq</span>)</span><br />
Method that returns the amino acid sequence as a list of three letter
codes.</td>
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<span class="codelink"><a href="Bio.SeqUtils-pysrc.html#seq3">source code</a></span>
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<td><span class="summary-sig"><a name="translate"></a><span class="summary-sig-name">translate</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">frame</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">genetic_code</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">translator</span>=<span class="summary-sig-default">None</span>)</span><br />
translation of DNA in one of the six different reading frames</td>
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<span class="summary-sig-arg">genetic_code</span>=<span class="summary-sig-default">1</span>)</span><br />
just an alias for six_frame_translations</td>
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<td><span class="summary-sig"><a name="six_frame_translations"></a><span class="summary-sig-name">six_frame_translations</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">genetic_code</span>=<span class="summary-sig-default">1</span>)</span><br />
nice looking 6 frame translation with GC content - code from xbbtools
similar to DNA Striders six-frame translation</td>
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<span class="codelink"><a href="Bio.SeqUtils-pysrc.html#six_frame_translations">source code</a></span>
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<td><span class="summary-sig"><a name="fasta_uniqids"></a><span class="summary-sig-name">fasta_uniqids</span>(<span class="summary-sig-arg">file</span>)</span><br />
checks and changes the name/ID's to be unique identifiers by adding
numbers</td>
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<td><span class="summary-sig"><a name="quick_FASTA_reader"></a><span class="summary-sig-name">quick_FASTA_reader</span>(<span class="summary-sig-arg">file</span>)</span><br />
simple and FASTA reader, preferable to be used on large files</td>
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<td><span class="summary-sig"><a name="apply_on_multi_fasta"></a><span class="summary-sig-name">apply_on_multi_fasta</span>(<span class="summary-sig-arg">file</span>,
<span class="summary-sig-arg">function</span>,
<span class="summary-sig-arg">*args</span>)</span><br />
apply function on each sequence in a multiple FASTA file</td>
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<td><span class="summary-sig"><a name="quicker_apply_on_multi_fasta"></a><span class="summary-sig-name">quicker_apply_on_multi_fasta</span>(<span class="summary-sig-arg">file</span>,
<span class="summary-sig-arg">function</span>,
<span class="summary-sig-arg">*args</span>)</span><br />
apply function on each sequence in a multiple FASTA file</td>
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<a name="proteinX"></a><span class="summary-name">proteinX</span> = <code title="ProteinX()">ProteinX()</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">reverse</span>(<span class="sig-arg">seq</span>)</span>
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<p>Reverse the sequence. Works on string sequences.</p>
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<p>Method that returns the amino acid sequence as a list of three letter
codes. Output follows the IUPAC standard plus 'Ter' for terminator. Any
unknown character, including the default unknown character 'X', is
changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized
(Sel, U).</p>
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